You Can't See It Until It's Too Late
by Mrs Doctor Who 11
Summary: The Doctor has come back after a year or so apart from Amy, but things are different and some are changes to do with him... Maybe oneshot, maybe twoshot, maybe more you decide- BIG TWIST IN THIS STORY!
1. Chapter 1

He didn't know how long it was since he'd left her.

No, _no_, since he'd left her _and_ Rory.

Why was it when he thought of her Rory seemed to evaporate?

And yet he was still there, a constant barrier, a black hole between two lone planets, bound to revolve around each other for eternity but never touch, because of that black hole.

They were bound together, could never leave each other and yet could never be together either.

He remembered how bad he'd felt, when she'd kissed him after the angels and he'd sort of lost control and let things get out of hand...

But he couldn't help it.

He loved her.

He loved his Mad, Impossible Amelia Pond, the pretty little Scottish girl who'd stole his heart and locked it up and left holding the key.

* * *

><p>And she loved him.<p>

She loved her Crazy, Raggedy Doctor, the man who'd dropped out of the sky into her grey life and filled it with colour, making the dark night seem no longer black but every shade of blue.

She loved him so much it hurt, and she missed him like crazy, and she knew it was wrong to stay married to Rory when she didn't love him but, once again, her Raggedy Man had left her and, once again, Rory was the one left standing there beside her.

Though one thing she was sure of.

He always left.

But he always came back.

* * *

><p>He shouldn't be doing this.<p>

Like, he REALLY shouldn't be doing this.

Amy could be living a happy life without him, and him coming back could screw it all up.

Though a little thought niggled at him.

_You never gave her the choice to stay. You only said that they had to leave, that they should get back to normal life. Maybe, if you'd given her the option, maybe she'd have stayed._

Yes, maybe she would.

And maybe one day he'd slip up, make a mistake and lose her, just like that, because he'd gone down the wrong corridor or left her in the wrong hands.

He'd rather she be with Rory and unhappy, than travel with him and be in danger constantly.

_"Come with me."_  
><em>"Where?"<em>  
><em>"Anywhere you like!"<em>

He said there was no reason he was taking her with him.

He'd lied.

Maybe it was the fact that she'd come to depend on him, to _need_ him that he loved her.

Or maybe it was the fact that, despite how long it had been, he couldn't stay away.

And maybe it had to do with the fact that she'd waited all her life for him and he didn't want to let her down.

Didn't want to have ruined her life and all she got after years of torture was twenty minutes of his time and then he was gone again.

He wanted to show her the world so that she, in turn, could show it to him.

* * *

><p>She was washing dishes in the sink in the kitchen.<p>

Tiny little kitchen in a tiny little cottage in a tiny little town.

Rory's dream.

Her worst nightmare.

Ever since she was a kid, she'd hated confined spaces, wanted to get out of Leadworth as soon as she was old enough.

That was something she loved about the Doctor.

His magic box.

_Big._

The inside, massive, endless rooms, countless staircases, tens of thousands of places to get lost in.

_Small._

The outside was tiny, the mere wrapping paper on the wonderful gift that was inside.

_Old._

An ancient box that rocketed through time and space, righting wrongs, leaving it's mark.

_New_.

A new TARDIS for a brand new Doctor, and yet it felt as if he was the only Doctor there ever was, couldn't imagine him in anothers body.

_Borrowed_.

Stolen away countless years ago with a madman out to see the universe, every intention of returning it, but now it had no home, and neither did he.

_The Bluest Blue You've Ever Seen._

So blue it was as if it were stood there, right in her backgarden, looking so out of place among the daffodils and daisies and yet, somehow, it fit right in...

There was a rapping on the window and she jumped, looked out at the person stood grinning at the window.

Floppy hair, green eyes, and the most beautiful smile she'd ever seen.

He was her Doctor.

And he'd come back.

* * *

><p>"Doctor!" she cried, running forward to hug him, grinning from ear to ear.<p>

"Amelia Pond! How are you? It's been a while!" he says, hugging her back.

"So, how long's it been? A year? Two?" he aks, holding her at armslength as though examining her.

"Erm, about a year and a half I think!" she says casually, but she lies.

She knows exactly how long since he left her.

One year, three months, two weeks, four days and two hours.

But she wouldn't tell him that.

He'd think she was mad.

* * *

><p>She was wrong.<p>

He knows exactly how long since he left her.

One year, three months, two weeks, four days and two hours.

For both of them.

But he wouldn't tell her that.

She'd think he was mad.

* * *

><p>"Come inside, come on, tell me what you've been up to!" she ushered him through the back door.<p>

"You first Pond, I mean look at you - little house in Leadworth, childhood sweetheart, every girls dream." he says as we walk through the kitchen.

"Not really. Every girls dream is to be whisked away by her knight in shining armour or her Prince Charming and live with him in his Palace forever."

There's an awkward silence, and then, as we enter the living room the Doctor breaks it.

"Well, I don't know about knights in shining armour, but a Centurion will do, eh?" he jokes and we both pretend to laugh as we flop into armchairs.

"So, what about you? Done anything special recently?" I say sarcastically.

"Oh, you know. Saved the world a few billion times, turned an entire species from evil to good, got banned from Sector 5 of Nartukkh. The usual." he says breezily.

Our conversation is stopped by a cry from upstairs.

"Ah, that's... that's Alexandra." I say, smiling a little uncomfortably.

"She's just woken up, I'd better get her." I leave him sat in the armchair.

I shouldn't care that he didn't look bothered about me having a baby.

I shouldn't care that he doesn't care I have a family.

I shouldn't care that he only thinks of me as a friend.

But I do.

And it hurts.

* * *

><p>She walks back into the room, a six month old baby in her arms.<p>

The baby is wearing sweet little dungarees with a cat face on them and a little multi-coloured stripy t-shirt.

Her tufty brown hair sticks up in wisps and is quite thick for a baby's.

Her large green eyes stare intelligently around, taking in everything.

Suddenly, the Doctor leaps up, eyes boggling.

"Blimey, Pond!" he practically chokes "I hope you're babysitting!"

"Wh-what?" Amy says, confused.

Why would he decide to care NOW?

She'd just told him she was getting the baby.

The Doctor holds out his arms and, reluctantly, Amy places the baby in them.

Eyes wide, the Doctor lifts the baby's face so it's next to his.

And suddenly she sees it.

Tufty brown hair, sticking up in wisps, quite thick, _his hair_.

Large, intelligent green eyes, _his eyes_.

"Oh God. Oh God, oh God, oh GOD..." she whispers in horror as she falls back into a chair, hand covering her mouth in shock.

"It can't be... How did I never notice it?... I..."

"There's only one way to find out." he says, grimly.

* * *

><p>Ten minutes later, Amy and the Doctor are sat opposite each other across the kitchen table, the baby gurgling in her highchair at the head of it.<p>

Solemnly, the Doctor lifts the spoon of baby mush and raises it to the baby's mouth.

The baby opens wide, swallows the mush, then starts squeaking and stretching her arms out for more.

"Oh God!" the Doctor lays his head on the table.

"Well, you never know! Maybe it's just a coincedence she looks exactly like you and likes fish fingers and custard..."

The Doctor lifts his head sharply, glaring in disbelief.

He grabs Amy's hand and places it on the baby's chest and sure enough, two beats pummel against her palm.

"There! Proof enough for you?" he spits, before resting his head on the table.

"Why are you acting like it's my fault?" she says, raising her voice.

"Because it bloody well is! How can you sit there and tell me that in six months you have never realised this baby looks exactly like me, likes fish fingers and custard and has two heart beats?" he yells.

The baby begins to cry and they both just look at her in shock, her starfish palms stretched out, her face scrunched up.

Amy reaches for her but the Doctor is quicker.

In a matter of seconds he's cradling the baby in his arms, soothing her, rocking her gently.

Amy watches and thinks how beautiful this moment is, and realises she can't miss out on a lifetime of this.

* * *

><p>"Amy?"<p>

"Mm?"

"Where's Rory?"

"At work."

"Right. Well, we'd better go."

"What? Go? What d'you mean go?"

"Well we can't stay here, can we? I really don't think a quiet life is my style, and besi-"

"No, I mean, what about Rory, he'll be worried sick!"

"Amy, do you really think he'd understand? All those times he was jelous and worried you were cheating on him, he's going to find out all of that's true. Do you really think he's going to understand? I just want you to be safe." he touches her face, and before he can move his hand away, she holds it there, sighing.

"OK. OK. But I have to leave him a note, explaining that I'm sorry but I don't love him and that Alexandra isn't his."

"OK. Get some stuff, be ready in five minutes."

"OK."

* * *

><p>Five minutes later, the Doctor almost walks into Amy coming out of the bathroom.<p>

"Come on Pond, we'd best be off, best to go as soon as- Amy what's up?" his jovial manner turns concerned as he sees her pale complexion even paler than usual, her eyes glassy and far away.

"Doctor," she gasps "I'm pregnant."

* * *

><p><strong>:O I'm pretty sure THIS doesn't happen in any other Amy and the Doctors baby story, I had the idea the other day and thought I'd put it out there! I might have this a oneshot, a twoshot, or maybe a few chapters long, you decide! R&amp;R what you thought and whether you think it should be a oneshot, twoshot or more! Thanks! :)<strong>

**Mrs Doctor Who 11 xx**


	2. Chapter 2

The TARDIS grated it's usual dematerialising sound as Amy followed the Doctor in, clutching her stomach.

Shifting Alexandra in his arms, the Doctor looks at Amy, concerned.

"Sure you're OK?"

"Yeah, I just... need to clear my head!" she smiles a smile that doesn't reach her eyes.

She walks off unsteadily out of the console room.

Closing his eyes he rests his head on the console.

"Take care of her old girl." he whispers.

* * *

><p>She opens a door to find herself in the medical bay.<p>

Her eyes widen, then she pushes the thought away.

_No, I'm just here for a scan, it's nothing like that._

After a quick scan, she's sure.

Pregnant.

Why was it always like this?

First, she got her saviour, her Doctor crashing in her backgarden, coming to whisk her away from boring old Leadworth, to take her somewhere exciting and new.

_Her Prince Charming._

Then, he'd disappeared and she'd got used to being crazy Amy, the one nobody liked.

_Locked away in a castle_.

Then Rory had appeared into her life as if to save her from the pain, to heal her wounds and say he believed her, that she wasn't crazy.

_Her Knight in Shining Armour._

Then the Doctor had come back into her life again, living up to his promise to save her from a life of loneliness - but he was too late; Rory got there first.

_What do you do if your knight in shining armour rescues you from the tower and then your Prince Charming shows up at your wedding?_

* * *

><p>He looked down at the baby.<p>

_His baby_.

He'd thought it would never happen again.

Never again.

After Gallifrey, he didn't think he'd ever have something like that again.

But he supposed it wasn't Mummy, Daddy, Baby.

He and Amy weren't together.

But he wanted to be.

Did she?

She'd left Rory for him, they had a baby together, she was the one who had kissed him...

But she was pregnant!

With _Rory's_ baby!

But Rory had a year and a half of being dad to Alexandra, so wasn't it the Doctor's turn by right to look after her?

One thing was certain.

He wasn't leaving this time.

He had to find Amy and tell her how he felt.

Whether she felt the same or not.

* * *

><p>She was sat on the bed when he walked in, after having put Alexandra in a bassinet that had conveniantely appeared in his room at the foot of his bed.<p>

"Oh, hey." he said, rubbing his hands together as he approached her.

Her face was tearstained and she stared at a screen.

"You see that?" she pointed at the screen sadly. "That's the baby. That little thing. I wanted to get rid of it. But I can't. I mean, something that tiny can't be bad... right?" her voice breaks on the last word and she begins to cry again.

He sits next to her on the med bay bed and pulls her into his side.

"Hey, shh, it's ok." he holds her as she cries quietly.

"What are we gonna do?" she says shakily.

"I think... I think we have to tell Rory. It's his baby and he deserves to know. I missed out on Alex and I wouldn't want him to go through the same."

He knew he was doing the right thing.

And it was breaking his heart.

* * *

><p><strong>:O keep reading, but i will be away for a week so just R&amp;R please - thanks for your reviews! I'm still working some stuff out but hopefully I will update as soon as I get back - due to popular demand, this story will be a proper dtory, not a few chapters long, but unfortuantely I have two other huge, time-consuming stories going at the minute so please understand if I don't update as much as the others. Thanks, R&amp;R, Byee!<strong>

**Mrs Doctor Who 11 xx**


	3. Chapter 3

**Twisty twist! BWAHAHA!**

* * *

><p>The Doctor smiled and held open the door.<p>

When Amy walked through it, the Doctor closed his eyes.

He was losing her all over again.

"Oi. Are you coming or what?" Amy said, trying to act like her old self, smiling a smile that didn't reach her eyes.

Fixing a grin on his face, he walks out the door and tries to pretend it isn't breaking his hearts.

* * *

><p>They walk across the garden, up to the house that Amy has just left - the one she had hoped she was leaving for good.<p>

The Doctor checked his watch - 5:30pm.

He told Amy this.

"Rory'll be back from work." she is about to open the door when she turns back to him. "But wait, if we're telling Rory about the baby, and he wants to be involved, where does that leave you?"

"We'll just... figure it out together." he said, and she threw her arms around him.

"I'm so sorry about all this." she whispered.

"Don't be stupid. Come on." he turned to the door.

She held her hand out, but he shook his head.

"You're about to tell him that the baby he's looked after for about a year isn't his." he said and Amy nodded, then finally opened the door.

Stepping in, she walked into the kitchen.

She could hear TV from the living room.

Suddenly Rory turned the corner, still wearing his scrubs.

He stared at Amy in disbelief.

"A-Amy! What are you doing here?" he asked bewildered.

"Um... I live here?" she said confused.

"Wh... Amy, it's been five years!" Rory said.

"Wha-" Amy turned to look at the Doctor, who's eyes wre wide with realization.

"Oops." he said, grinning sheepishly.

"Seriously? Five years? Could this get ANY worse?" Amy said - as a blonde woman walked into the room holding a toddler in each arm.

"Rory, I'm going to change Jake's nappy, could you get Ella and-" she stopped speaking as she saw the people stood in her kitchen.

"Oh... hello. Rory, who's this?" she said smiling uncertainly.

"THIS, is his wife." Amy said heatedly.

"What? I'm sorry, you must be mistaken." she held up a hand on which an engagement ring and a wedding ring glimmered.

Amy's mouth dropped open, as did the Doctor's.

She was so stunned, that when Rory asked why she was here, she answered without thinking.

"I'm pregnant."

There was a silence.

"Rory." the womans voice rang out with fury. "Why is there a woman in our kitchen saying she's your wife and she's pregnant?"

"I'll explain everything. Don't worry, it's not what you think, Sarah." Rory took Sarahs hands and she nodded; Amy had to give her credit, if she'd been in her shoes she would have left already.

Rory told her about how Amy and him had been married and had a baby, and then one day she'd just disappeared with Alex without any explanation.

After the Doctor told them their story, Rory stood, struggling to take it all in.

Then he punched the Doctor in the face.

Doubling over, the Doctor clutched his nose and cursed.

"Ouch... I guess I deserve that." he straightened up, still clutching his nose, and Rory punched him again.

"OOOOOW! Not sure I deserved THAT!" he complained.

"Rory stop! We have to think of what to do now." Amy said.

"Right. Yeah. Well." Rory said, trying to gather his thoughts.

Suddenly Amy doubled over, gasping.

"Amy? Amy?" the Doctor said, holding her arm, panicing.

"I- OW!" Amys breath hissed as she withdrew it sharply.

Her vision clouded and her hearing became muted.

"We have to get her to the TARDIS. Quickly." she felt the Doctor lift her in his arms as she passed out.

* * *

><p>Amy awoke on the med-bay bed, Rory and Sarah (who was holding the twins) at her side as the Doctor set up the scanner.<p>

Running it over her stomach, he stared intently at the screen.

He gagged as he looked at it.

"What? What is it?" Amy said, stretching her neck to try and see.

The Doctor switched off the scanner and darted around, looking for something.

"Doctor what is it?" Amy asked, agitated.

He said nothing.

"Doctor PLEASE!" she said, terrified.

He turned to her, eyes wide and frantic.

"Amy, that's not a baby, it's a Silent! It's been implanted inside you, and it's gonna grow and grow, feeding off you until you just die! And I don't know how to stop it."


	4. Chapter 4

The Doctor was dashing around shelves, Rory was pulling vials off cabinets and yelling their contents to the Doctor, Sarah was shifting a wailing Jake in one arm and a shrieking Ella in the other.

Amy was in a haze.

She could see them and hear them, but her senses were clouded, her eyes bleary and hearing muffled.

Suddenly, the Doctors face appeared.

"Got it!" he grinned, brandishing a small needle and Amy snapped out of her trance.

"No!" she screamed, jumping from the table, a hand placed protectively over her stomach.

"Amy..." the Doctor warned, taking a step closer.

"Don't come near me!" Amy said, voice wavering.

"Amy, I have to get rid of it, it's not a baby it's a monster that will kill you!" the Doctor said, urgently.

"No!" she said again.

Realization lit the Doctors eyes and he looked disgusted.

"It's a survival technique of the Silent, they're making her reject the idea of anything damaging it. She understands what it is and what will happen but she's had her free will taken away - she can't say no to it."

The Doctor took a tentative step forward, as though he was just checking to see if the ground was stable.

When Amy began to back away, the Doctor pocketed the needle and held up his hands.

"Amy, I promise, I won't hurt you." he began to walk towards her and she let him, now the needle was out of sight.

Closing his eyes, cupping her face in his palms and pressing his forehead to Amys, he spoke quietly.

"Amy, I need you to let me do this. I need you to trust me."

"I... I can't do it!" Amy whispered back, tears rolling from her closed eyelids.

"Then I will." the Doctor said sadly, and in one swift movement he had pulled the needle from his pocket, jabbed it into Amy's side and released the fluid inside it into her body.

Amy staggered back from him.

"You tricked me!" she said horrified.

"No Amy. I saved you."

* * *

><p><strong>I resolved it - maybe a little too quickly, but meh. The story isn;t over yet and I know its not very Doctor like to tell someone he saved them, but I think he needed to let Amy know he was helping her not hurting her. Review for a preview!<strong>

**Mrs Doctor Who 11 xx**


	5. Chapter 5

"And here," the Doctor flipped a switch "Is the neutron flow!"

The baby in his arms stretched a hand towards the lever and smacked it back down.

The TARDIS lurched and the Doctor yelled "No, no, that'll send us into a Time Warp! We need to reverse the polarity of the neutron flow!" he flipped the switch again and the TARDIS stopped juddering.

The baby in his arms giggled.

"That, was NOT funny!" the Doctor said moodily, wagging a finger in front of Alexandras face.

Green eyes wide, she grabbed his finger.

She then jabbed it, very forcefully, into the Doctors eye.

"OW! AMY! Come and get her please!" the Doctor yelled, holding Alex in one arm and shielding his wounded eye with the other.

Amy walked in, still pale and a little unsteady from the shock of before, but she managed to shoot him a small smile.

She held out her arms for Alex, but instead the Doctor placed her on the floor, grabbed a little spaceship that had been hiding among the wires on the console, gave it to her and then straightened up to look at Amy.

Taking Amy's hand gently, he led her to the other side of the Console were she sat in a chair and the Doctor grabbed one out of nowhere and sat next to her.

Still holding her hand, he looked into her eyes, his expression concerned.

"Hey, listen. I know before, when I said I saved you, I want you to know I wasn't bragging. It's just, I needed you to know that I _was_ saving you, not tricking you, that I'd never do anything to hurt you. You understand?" he said gently.

She smiled, and it was a glimmer of Amy, _his_ Amy.

"Course I do. I'm just being silly, that _thing_ messing with my mind." she smiled.

"I know what you need! A trip to cheer you up!" the Doctor beamed, springing up and bashing a button.

"Where?" Amy said curiously.

He looked at her out of the corner of his eye, grinning mischeviously.

"Surprise!" he said excitedly.

He pulled a lever and... waltz music spread through the TARDIS.

"Oh, well... in that case... may I have this dance, Miss Pond?" the Doctor said, feigning snootiness as he held a hand out to her.

"Why of course, Sir Doctor!" she said, mimicing his tone and courtsying.

They began to dance, quite slowly at first but getting a little faster until they were laughing and spinning and out of breath.

When they finally stopped, Amy was so dizzy, the Doctor had to steady her with a hand on her waist.

"I'm fine!" she laughed "It's just- oh my God!" her tone changed to hushed amazement as the Doctor turned to see what she was looking at.

It was Alex, standing unsteadily on her stripy-socked feet.

Simultaneously, Amy and the Doctor crouched down; Alex was a few metres away.

"Has she ever...?" the Doctor asked.

"No, this is the first time." Amy said, shocked.

Amy held out her arms to Alex as the Doctor crouched beside Amy and watched.

Alex took her first, shaky step.

Then another.

Then another.

She was halfway.

She was almost there.

Amy knew her baby could fall at any moment, but didn't doubt that at the slightest falter, the Doctor would be swooping Alex up in an instant.

Alex was a few centimetres away from Amy.

Then, at the last moment, she turned and flopped into the Doctor's lap.

His eyes widened in amazement, then a grin split his face as he scooped the babbling Alex up in his arms.

"Who's my clever girl then? Who's my clever girl?" he cooed to the baby, euphoric.

Amy watched smiling.

She wasn't sad her daughter had gone to the Doctor.

She had gone to her Daddy, who needed Alex's attention after missing her first year.

The Last Timelord and his daughter.

It reminded Amy of something, but she couldn't think what.

The Doctor and Alex.

Apart, they were alone, the Doctor thinking he was the last of his kind and Alex not even knowing what true species she was.

But together, they were complete.

Then she remembered what the Doctor had said at her wedding to Rory.

_"2000 years. The Boy Who Waited. Good on you mate."_

And I was The Girl Who Waited.

The Doctor turned as she approached him.

"Doctor, you said me and Rory were meant for each other. The Girl Who Waited and The Boy Who Waited. But the thing is, he waited for me... but who did I wait for?" Amy smiled as the Doctor's face mirrored hers as he understood what she meant.

It was as their lips moulded together, as though made for each other, that Amy thought of something.

_Looks like I got my happy ending._

* * *

><p><strong>THE END.<strong>

**Bwahaha, just kidding, there will be a sequel! Well that depends on how many reviews I have for this chapter... Yes more blackmail! If there are no reviews, I won't write a sequel.**

**If there are loads of reviews I update MEGA fast.**

**And any reviewers get a sequel preview! **

**Mrs Doctor Who 11 xx**


	6. Chapter 6

Sequel up! It's called Reality Hopping, weird title I know but it will be to do with the story arc and I'm sick of long titles - there may be lot's of Torchwood, which I've just discovered but not to do with Miracle Day and it will still be mostly about Alex. Find it at my profile. Now. GOGOGO!

Mrs Doctor Who 11 xx 


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